## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Kyi_1_2016-10-03/UA_Kie_Kyi_1_2016-10-03.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Kyi_1_2016-10-03/UA_Kie_Kyi_1_2016-10-03.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Kyi_1_2016-10-03/UA_Kie_Kyi_1_2016-10-03.mark_duplicates_report.txt REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=SILENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Fri Jan 20 17:21:20 UTC 2023

## METRICS CLASS	picard.sam.DuplicationMetrics
LIBRARY	UNPAIRED_READS_EXAMINED	READ_PAIRS_EXAMINED	SECONDARY_OR_SUPPLEMENTARY_RDS	UNMAPPED_READS	UNPAIRED_READ_DUPLICATES	READ_PAIR_DUPLICATES	READ_PAIR_OPTICAL_DUPLICATES	PERCENT_DUPLICATION	ESTIMATED_LIBRARY_SIZE
lib1	25499275	8206969	0	0	6264301	760868	0	0.185766	41481359

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	6686158	6686158
2.0	1.820495	451590	451590
3.0	2.493708	36864	36864
4.0	3.046075	5082	5082
5.0	3.49929	1758	1758
6.0	3.871151	1088	1088
7.0	4.176261	743	743
8.0	4.426602	555	555
9.0	4.632006	408	408
10.0	4.800539	327	327
11.0	4.93882	236	236
12.0	5.052278	248	248
13.0	5.14537	209	209
14.0	5.221752	183	183
15.0	5.284422	156	156
16.0	5.335844	157	157
17.0	5.378034	127	127
18.0	5.412652	130	130
19.0	5.441055	109	109
20.0	5.46436	116	116
21.0	5.483481	87	87
22.0	5.49917	86	86
23.0	5.512043	89	89
24.0	5.522605	85	85
25.0	5.531271	85	85
26.0	5.538382	72	72
27.0	5.544216	83	83
28.0	5.549003	55	55
29.0	5.55293	65	65
30.0	5.556153	64	64
31.0	5.558797	64	64
32.0	5.560967	67	67
33.0	5.562747	51	51
34.0	5.564207	59	59
35.0	5.565406	46	46
36.0	5.566389	51	51
37.0	5.567196	29	29
38.0	5.567858	39	39
39.0	5.568401	37	37
40.0	5.568846	37	37
41.0	5.569212	29	29
42.0	5.569512	36	36
43.0	5.569758	21	21
44.0	5.56996	29	29
45.0	5.570126	25	25
46.0	5.570262	14	14
47.0	5.570373	20	20
48.0	5.570465	21	21
49.0	5.57054	19	19
50.0	5.570602	14	14
51.0	5.570652	20	20
52.0	5.570694	19	19
53.0	5.570728	16	16
54.0	5.570756	20	20
55.0	5.570778	16	16
56.0	5.570797	22	22
57.0	5.570813	11	11
58.0	5.570825	9	9
59.0	5.570836	14	14
60.0	5.570844	18	18
61.0	5.570851	16	16
62.0	5.570857	15	15
63.0	5.570862	13	13
64.0	5.570866	8	8
65.0	5.570869	13	13
66.0	5.570871	16	16
67.0	5.570873	17	17
68.0	5.570875	11	11
69.0	5.570877	9	9
70.0	5.570878	13	13
71.0	5.570879	10	10
72.0	5.57088	14	14
73.0	5.57088	14	14
74.0	5.570881	19	19
75.0	5.570881	11	11
76.0	5.570882	13	13
77.0	5.570882	10	10
78.0	5.570882	11	11
79.0	5.570882	10	10
80.0	5.570882	9	9
81.0	5.570883	20	20
82.0	5.570883	12	12
83.0	5.570883	9	9
84.0	5.570883	3	3
85.0	5.570883	10	10
86.0	5.570883	10	10
87.0	5.570883	8	8
88.0	5.570883	5	5
89.0	5.570883	6	6
90.0	5.570883	10	10
91.0	5.570883	8	8
92.0	5.570883	3	3
93.0	5.570883	6	6
94.0	5.570883	6	6
95.0	5.570883	5	5
96.0	5.570883	5	5
97.0	5.570883	12	12
98.0	5.570883	8	8
99.0	5.570883	5	5
100.0	5.570883	6	6
101.0	0	7	7
102.0	0	9	9
103.0	0	8	8
104.0	0	7	7
105.0	0	2	2
106.0	0	7	7
107.0	0	4	4
108.0	0	9	9
109.0	0	4	4
110.0	0	4	4
111.0	0	5	5
112.0	0	8	8
113.0	0	6	6
114.0	0	5	5
115.0	0	4	4
116.0	0	2	2
117.0	0	5	5
118.0	0	4	4
119.0	0	4	4
120.0	0	4	4
121.0	0	2	2
122.0	0	2	2
123.0	0	6	6
124.0	0	4	4
125.0	0	1	1
126.0	0	3	3
127.0	0	8	8
128.0	0	2	2
130.0	0	2	2
132.0	0	6	6
133.0	0	4	4
134.0	0	4	4
135.0	0	3	3
136.0	0	6	6
137.0	0	3	3
138.0	0	3	3
139.0	0	2	2
140.0	0	4	4
141.0	0	2	2
142.0	0	2	2
143.0	0	3	3
144.0	0	1	1
145.0	0	6	6
146.0	0	2	2
147.0	0	2	2
148.0	0	5	5
149.0	0	2	2
150.0	0	1	1
151.0	0	7	7
153.0	0	2	2
154.0	0	7	7
155.0	0	1	1
156.0	0	1	1
157.0	0	1	1
158.0	0	3	3
159.0	0	2	2
160.0	0	2	2
162.0	0	2	2
163.0	0	2	2
164.0	0	1	1
165.0	0	1	1
167.0	0	1	1
169.0	0	1	1
172.0	0	2	2
174.0	0	2	2
175.0	0	4	4
176.0	0	2	2
177.0	0	1	1
180.0	0	1	1
181.0	0	1	1
182.0	0	1	1
183.0	0	2	2
184.0	0	2	2
186.0	0	1	1
187.0	0	1	1
189.0	0	1	1
191.0	0	2	2
192.0	0	3	3
195.0	0	1	1
198.0	0	3	3
202.0	0	1	1
203.0	0	1	1
204.0	0	1	1
205.0	0	2	2
206.0	0	1	1
208.0	0	1	1
209.0	0	1	1
211.0	0	3	3
213.0	0	1	1
214.0	0	2	2
215.0	0	2	2
216.0	0	1	1
217.0	0	1	1
222.0	0	1	1
223.0	0	2	2
224.0	0	1	1
230.0	0	2	2
231.0	0	1	1
232.0	0	1	1
233.0	0	2	2
234.0	0	1	1
236.0	0	1	1
237.0	0	1	1
238.0	0	1	1
239.0	0	1	1
240.0	0	1	1
241.0	0	1	1
242.0	0	2	2
244.0	0	1	1
246.0	0	1	1
248.0	0	2	2
251.0	0	1	1
252.0	0	1	1
256.0	0	1	1
259.0	0	1	1
260.0	0	1	1
261.0	0	1	1
265.0	0	3	3
266.0	0	1	1
269.0	0	1	1
272.0	0	1	1
276.0	0	1	1
277.0	0	1	1
279.0	0	1	1
285.0	0	1	1
287.0	0	1	1
289.0	0	2	2
291.0	0	1	1
292.0	0	1	1
293.0	0	1	1
294.0	0	1	1
295.0	0	2	2
296.0	0	1	1
302.0	0	1	1
307.0	0	1	1
310.0	0	2	2
315.0	0	1	1
317.0	0	2	2
322.0	0	1	1
324.0	0	1	1
326.0	0	1	1
330.0	0	2	2
333.0	0	1	1
334.0	0	1	1
336.0	0	1	1
338.0	0	1	1
342.0	0	1	1
359.0	0	1	1
363.0	0	1	1
364.0	0	1	1
366.0	0	2	2
368.0	0	1	1
377.0	0	1	1
383.0	0	1	1
384.0	0	1	1
386.0	0	1	1
391.0	0	1	1
395.0	0	1	1
409.0	0	1	1
426.0	0	1	1
442.0	0	1	1
451.0	0	1	1
453.0	0	1	1
459.0	0	1	1
461.0	0	1	1
468.0	0	1	1
477.0	0	1	1
507.0	0	1	1
511.0	0	1	1
513.0	0	1	1
514.0	0	1	1
543.0	0	1	1
554.0	0	1	1
593.0	0	1	1
621.0	0	1	1
679.0	0	1	1
695.0	0	1	1
705.0	0	1	1
713.0	0	1	1
754.0	0	1	1
756.0	0	1	1
808.0	0	1	1
900.0	0	1	1
916.0	0	1	1
976.0	0	1	1
1319.0	0	1	1
2127.0	0	1	1
4628.0	0	1	1